Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0E1-N1-BDNA-1_A23MHW3LT4_1/1136_0E1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/b593eae42aa14aef658ddc3220bb72/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/b593eae42aa14aef658ddc3220bb72/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_0E1-N1-BDNA-1_A23MHW3LT4_1/1136_0E1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_0E1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0E1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_0E1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0E1-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 63020174 total, 55871 skipped (flags/unmapped)
Fragments: 31721631 total (31208587 tlen-paired, 3500 hash-paired, 392 singletons, 10959 discordant, 498193 orphans, 9813 too large [>5000 bp], 12048740 duplicates)
Reads: 66570508 total, 45680 skipped (flags/unmapped)
Fragments: 33516695 total (32982183 tlen-paired, 2257 hash-paired, 447 singletons, 7419 discordant, 524389 orphans, 8137 too large [>5000 bp], 12346398 duplicates)
Reads: 72357226 total, 50392 skipped (flags/unmapped)
Fragments: 36431082 total (35822354 tlen-paired, 3061 hash-paired, 315 singletons, 11131 discordant, 594221 orphans, 19603 too large [>5000 bp], 13790927 duplicates)
Reads: 73830931 total, 86830 skipped (flags/unmapped)
Fragments: 37438895 total (35660064 tlen-paired, 3122 hash-paired, 431 singletons, 349882 discordant, 1425396 orphans, 146069 too large [>5000 bp], 14026330 duplicates)